Hi Bruce,

Thanks for your answer. I was trying to use the fsl segment in freesurfer indeed. But since I couldn't get that working, I am now trying to do the trick with mri_segment. Sorry to ask you again, but I still have troubles with mri_segment. So I am trying to use the -wm_low flag to make the program do a different segmentation than the default. But it looks like mri_segment is still using the default settings? And the wm.new.mgz I get out of it looks completely the same as my previous wm.mgz

So my command is: mri_segment brain.mgz wm.new.mgz -wlo 110

This is what comes out:

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (104.0): 105.4 +- 4.8 [80.0 --> 125.0]
GM (70.0) : 68.4 +- 10.3 [30.0 --> 96.0]
setting bottom of white matter range to 78.6
setting top of gray matter range to 88.9
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...

reclassifying voxels using Gaussian border classifier...

removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
3683 sparsely connected voxels removed...
thickening thin strands....
20 segments, 2500 filled
8702 bright non-wm voxels segmented.
4341 diagonally connected voxels added...
white matter segmentation took 1.5 minutes
writing output to wm.new.mgz...

I put the output in bold which (I think) could be causing troubles(?) It looks like mri_segment is still using the default limits for wm and gm. I tried the same adding the flag -noauto, but it didn't make any difference.

Do you know what I am doing wrong here? How should I use mri_segment in order to really set different ranges of wm and gm intensities?

Again, thanks for your help!!

Doety